Updating to Version 0.3.0

phac-nml / irida-plugin-amr-detection

IRIDA Plugin for AMR Detection

Apache License 2.0

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Updating to Version 0.3.0 #18

Closed emarinier closed 1 year ago

emarinier commented 1 year ago

Updates the IRIDA AMR detection plugin from version 0.2.0 to 0.3.0.

Updates staramr to version 0.9.1
Updates shovill to version 1.1.0
Updates RGI to version 5.2.1
RGI 5.2.1 is difficult to install with Conda (because of dependency resolution) and may need a manual installation using mamba.

apetkau commented 1 year ago

Another comment I could make, is that for some reason increasing the number of cores assigned to shovill for me caused spades to crash (ran out of memory). I suspect this is more of a shovill (or spades) issue rather than an issue with your additions.

Also, here's, in brief, what I had to do to get rgi installed:

Run the following in the Galaxy machine (using the Galaxy conda) prior to installing the rgi tool in Galaxy:

conda install -c conda-forge -c bioconda -c defaults mamba -y
mamba create -c iuc -c conda-forge -c bioconda -c defaults --no-channel-priority --name __rgi@5.2.1 rgi=5.2.1 -y

Install RGI in Galaxy as normal

Maybe this could be added to the README.md too?

emarinier commented 1 year ago

I did have a few in-line comments for you. Another more general comment is: could you update both the README.md and CHANGELOG.md files to include information about the new version (such as the necessary tool versions to install in Galaxy)? Updating the README.md could also be done as another PR if you wanted too (though it's nice to update the CHANGELOG.md with the changes in this same PR).

I think I've everything that needed to be updated in the README and CHANGELOG:

CHANGELOG in 09a6d78
README in 6b23cd5

emarinier commented 1 year ago

Also, here's, in brief, what I had to do to get rgi installed:

1. Run the following in the Galaxy machine (using the Galaxy conda) prior to installing the rgi tool in Galaxy:
   ```shell
   conda install -c conda-forge -c bioconda -c defaults mamba -y
   mamba create -c iuc -c conda-forge -c bioconda -c defaults --no-channel-priority --name __rgi@5.2.1 rgi=5.2.1 -y
   ```

2. Install RGI in Galaxy as normal

Maybe this could be added to the README.md too?

Added instructions in 09a6d78 and fixed some typos in 49f37db.

apetkau commented 1 year ago

Thanks so much for all your changes Eric. This looks awesome.

The only other general comment that I forgot about before, is I'm wondering if you could add information in the README file about installing the RGI database? Possibly include a screenshot of the database installation tool?

emarinier commented 1 year ago

Thanks so much for all your changes Eric. This looks awesome.

The only other general comment that I forgot about before, is I'm wondering if you could add information in the README file about installing the RGI database? Possibly include a screenshot of the database installation tool?

Updated!

apetkau commented 1 year ago

Thanks @emarinier . Looks great. Merging this in.